On 06/10/2021 11:19 AM, James Holton wrote:
I'm afraid the only bash command I know is: "tcsh"
I learned csh by studying "elves"
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Dear Colleagues,
I commend to you the European Crystallography School ECS6.
Full details are here:-
https://akcongress.com/ecs6/
Best wishes,
John
Emeritus Professor John R Helliwell DSc
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Many thanks, James, for the tips. This one worked also,
peakmax MAPIN "mymap.ccp4" XYZOUT "mypeaks_output.pdb" <<- EOF
EOF
Best regards,
On Thu, Jun 10, 2021 at 5:19 PM James Holton wrote:
>
> I'm afraid the only bash command I know is: "tcsh"
>
> However, in addition to suggestions so far
On Thu, Jun 10, 2021 at 08:19:01AM -0700, James Holton wrote:
> I'm afraid the only bash command I know is: "tcsh"
I'm using the exact opposite direction ;-)
To everyone using "echo" (interactively and/or in scripts): be careful
which command is picked up at any given point. There are shell
Dear all
Halic lab is looking for highly motivated and enthusiastic postdoctoral
candidate interested in cryo-EM of chromatin complexes. Strong background in
molecular cloning, expression, and purification of protein complexes is
essential. Experience in X-ray crystallography or single particle
I'm afraid the only bash command I know is: "tcsh"
However, in addition to suggestions so far, I expect this will work:
echo "" | peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"
Your peakmax is waiting for options to come in on "standard input". The
vertical bar "|" is a "pipe" tha
Tim,
can I explain? To be honest no! Other than old habits and all. Should converge
to the same value in the end, so you have a valid point.
All the best Graeme
From: Tim Gruene
Sent: Thursday, June 10, 2021 14:02
To: Winter, Graeme (DLSLtd,RAL,LSCI)
Cc: CCP4BB
A funded postdoctoral position in structural biology is available immediately
in the laboratory of Professor Celia Goulding at the University of California,
Irvine. Our studies focus on the structural biology and biochemistry of
Mycobacterium tuberculosis iron/heme uptake and bacterial contact-
Correct me if I'm wrong, but the first papers to stop reporting R-anything were
XFEL ones so I assumed it was a particularly bad estimator of data quality for
those expt's ;-
With a more normal expt, again correct this if it's wrong, the problems with
R-merge only throw it off by a few percent?
Or just boycott the journal...??
On 10/06/2021 14:02, Tim Gruene wrote:
Hi Graeme,
could you explain why Rmeas does not serve the same purpose as Rmerge?
I guess Manfred (and others) have no objection to reporting Rmeas just
instead of Rmerge.
@ Christy: If one of my manuscript were rejected
Hi Graeme,
could you explain why Rmeas does not serve the same purpose as Rmerge?
I guess Manfred (and others) have no objection to reporting Rmeas just
instead of Rmerge.
@ Christy: If one of my manuscript were rejected solely because Rmerge
was not mentioned, I would make a phone call to the bo
Dear Manfred,
I completely agree. However this is not routinely reported.
The discussion is of removing one indicator of this signal, rather than
replacing it with a superior measure - the latter is something I would more
actively support however would involve adding new stuff which is an uphil
Dear Graeme,
a better number to look at is Isa. Instead of low resolution Rmerge.
Seriously. We monitor that to assess beamline performance.
Cheers, Manfred
Am 10.06.2021 um 14:42 schrieb Winter, Graeme (DLSLtd,RAL,LSCI):
Once again I find myself jumping to the defence of this rather poor stati
Once again I find myself jumping to the defence of this rather poor statistic!
Yes, Rmerge is a very poor estimator of "data quality" and has many well
published flaws related to multiplicity, but the low resolution Rmerge, if
combined with a multiplicity > (say) 5, is a good indicator of whethe
An NIH-funded postdoctoral research position is available immediately in the
Hughson lab at Princeton University. Our group’s research focuses on the
remarkable protein machinery that generates the interior architecture of
eukaryotic cells by orchestrating the formation and fusion of cargo-carry
Dear Cristy,
this is really hilarious. And it just shows how attached
some ppl are to outdated numbers. Against better
knowledge.
It has been shown many times that Rmerge is flawed
at various levels.
The only reason I can see to report it is to be backwards
compatible. But of course, this is a
Dear all
We have an opportunity for a scientist with a keen interest in beamline
development, automation and/or structural biology to join the macromolecular
crystallography leadership team at Diamond to guide and develop the I03
beamline. I03 is at the forefront of cryogenic automated data col
Dear Colleagues
Hope to find you all well and healthy.
I have a question regarding Rmerge. In recent years, we have published our
crystallographic structures in highly respected journals using CC1/2,
I/sigma(I), completeness and multiplicity as quality parameters for our
diffraction data.
Recentl
some info here:
https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Topology_plots
(haven’t done it myself for a while, so not sure which programs are still being
maintained)
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28
On 10/06/2021 12:14, Gambelli, Lavinia wrote:
I'm looking for a software to make topology diagrams of proteins. Ideally, I'd like to submit a pdb file and
obtain the topology model. Do you know what alternatives are out there? So far I'm only aware of PDBsum that
can do this, but I was wonderi
Hello,
I'm looking for a software to make topology diagrams of proteins. Ideally, I'd
like to submit a pdb file and obtain the topology model. Do you know what
alternatives are out there? So far I'm only aware of PDBsum that can do this,
but I was wondering if there is something else available.
I'd like to draw your attention to an opening at SPT Labtech for a US-based
Field Applications Scientist position in CryoEM. Please find a description
below.
For more info and to apply, please visit:
https://apply.workable.com/spt-labtech/j/20D368B245/?utm_medium=social_share_link
Applications
Dear Paul
Thank you. I installed it through curlew. Now it works fine. It is Shift +
c for the dialogue box to appear then type the amino acid code you want to
mutate the residue with and boom..new amino acid appears at its original
position.
Thanks
Firdous
On Thu, Jun 10, 2021 at 1:14 AM Paul
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